Comparative genomic analysis demonstrates that true reinfection following SARS-CoV-2 infection is possible.

Background: In recent months, multiple cases of confirmed SARS-CoV-2 reinfection have been reported. However, accurate epidemiological and virological data, including genomic analysis where possible, are required to differentiate cases of prolonged viral RNA shedding (i.e. intermittent detection) from true reinfection. The objective of this review was to systematically identify and summarise all cases of SARS-CoV-2 reinfection confirmed by comparative genomic analysis. Methods: A protocol based on Cochrane rapid review methodology was employed. Databases and pre-print servers were searched until 9/11/2020. Results: Ten studies, representing 17 patients, were identified (mean age=40; 71% male). The time interval between primary infection and reinfection ranged from 13 to 142 days (median: 60).Comparative whole genome sequencing confirmed reinfection in 14 patients (the primary and secondary infections were caused by different viruses). A further three cases had strong, but not confirmed evidence of reinfection, as only partial genomes were retrieved on primary infection.Across 12 studies that reported the number of single nucleotide polymorphisms (SNPs) comparing the first and second genomes, between 8 and 24 SNPs were discovered. With an average SARS-CoV-2 mutation acquisition rate of 1-2 per month, in all cases it is likely that the secondary infection was caused by a different SARS-CoV-2 virus, rather than prolonged shedding of viral RNA from the primary infection.In five reinfection cases, the primary and secondary infections were caused by different SARS-CoV-2 lineages/clades, strongly indicating that infections were caused by different viruses. Conclusion: Comparative genomic analyses from 14 patients confirm that SARS-CoV-2 reinfection can occur.

The perception of risk in contracting and spreading COVID-19 amongst individuals, households and vulnerable groups in England: a longitudinal qualitative study.

BACKGROUND: Social distancing restrictions to manage the COVID-19 pandemic were put in place from March 2020 in the United Kingdom (UK), with those classed as "highly clinically vulnerable" advised to shield entirely and remain at home. However, personal risk perception has been shown to comprise of various elements beyond those outlined in the national pandemic guidance. It is unclear whether those deemed COVID-19 vulnerable identified as high-risk to COVID-19 and thus complied with the relevant advice. The aim of this research is to explore the perception of risk in catching and spreading COVID-19, amongst individuals from individual households, and vulnerable groups in a region of the UK. METHODS: Two individual, semi-structured interviews were conducted, four-weeks apart, with adults living in households in the Liverpool City Region. At the follow-up interview, participants were given the option of using photo-elicitation to guide the discussion. Reflexive thematic analysis was employed to conceptualise themes. The qualitative analysis was underpinned with symbolic interactionism. RESULTS: Twenty-seven participants (13:14 males:females, and 20 with a vulnerable risk factor to COVID-19) completed a baseline interview, and 15 of these completed a follow-up interview four-weeks later. Following thematic analysis, two overarching themes were conceptualised, with subthemes discussed: theme 1) Confusion and trust in the risk prevention guidance; and theme 2) Navigating risk: compliance and non-compliance with public health guidance. CONCLUSION: Participants developed their own understanding of COVID-19 risk perception through personal experience and comparison with others around them, irrespective of vulnerability status. COVID-19 guidance was not complied with as intended by the government, and at times even rejected due to lack of trust. The format in which future pandemic guidance is conveyed must be carefully considered, and take into account individuals' experiences that may lead to non-compliance. The findings from our study can inform future public health policy and interventions for COVID-19 and future pandemics.

Perspectives on the production, and use, of rapid evidence in decision making during the COVID-19 pandemic: a qualitative study.

OBJECTIVES: To describe perceptions of providing, and using rapid evidence, to support decision making by two national bodies (one public health policy and one front-line clinical practice) during the COVID-19 pandemic. DESIGN: Descriptive qualitative study (March-August 2020): 25 semistructured interviews were conducted, transcribed verbatim and thematically analysed. SETTING: Data were obtained as part of an evaluation of two Irish national projects; the Irish COVID-19 Evidence for General Practitioners project (General Practice (GP) project) which provided relevant evidence to address clinical questions posed by GPs; and the COVID-19 Evidence Synthesis Team (Health Policy project) which produced rapid evidence products at the request of the National Public Health Emergency Team. PARTICIPANTS: Purposive sample of 14 evidence providers (EPs: generated and disseminated rapid evidence) and 11 service ssers (SUs: GPs and policy-makers, who used the evidence). MAIN OUTCOME MEASURES: Participant perceptions. RESULTS: The Policy Project comprised 27 EPs, producing 30 reports across 1432 person-work-days. The GP project comprised 10 members from 3 organisations, meeting 49 times and posting evidence-based answers to 126 questions. Four unique themes were generated. 'The Work' highlighted that a structured but flexible organisational approach to producing evidence was essential. Ensuring quality of evidence products was challenging, particularly in the context of absent or poor-quality evidence. 'The Use' highlighted that rapid evidence products were considered invaluable to decision making. Trust and credibility of EPs were key, however, communication difficulties were highlighted by SUs (eg, website functionality). 'The Team' emphasised that a highly skilled team, working collaboratively, is essential to meeting the substantial workload demands and tight turnaround time. 'The Future' highlighted that investing in resources, planning and embedding evidence synthesis support, is crucial to national emergency preparedness. CONCLUSIONS: Rapid evidence products were considered invaluable to decision making. The credibility of EPs, a close relationship with SUs and having a highly skilled and adaptable team to meet the workload demands were identified as key strengths that optimised the utilisation of rapid evidence. ETHICS APPROVAL: Ethical approval was obtained from the National Research Ethics Committee for COVID-19-related Research, Ireland.

Consensus recommendations for opioid agonist treatment following the introduction of emergency clinical guidelines in Ireland during the COVID-19 pandemic: A national Delphi study.

BACKGROUND: Emergency contingency guidelines for opioid agonist treatment (OAT) were introduced in Ireland in March 2020, to ensure rapid and uninterrupted access to treatment while mitigating COVID-19 risk. The contingency guidelines deviated, across multiple clinical domains, from pre-pandemic clinical guidelines published in 2016. The objectives of this study are to (1) identify changes introduced to OAT clinical guidelines in Ireland during the pandemic; and (2) develop consensus on whether the new recommendations should be retained beyond the pandemic, using a national Delphi consensus methodology. METHODS: Clinical guidance recommendations ('statements') were generated by comparing the newly established contingency guidelines with the national 2016 Clinical Guidelines for OAT. Over two rounds of on-line Delphi testing, a panel of experts (people currently accessing OAT, psychiatrists, general practitioners, community pharmacists, a nurse, a psychologist and support/key workers) independently rated their agreement with each statement and provided comments. Statements with a median score of 4 or 5 and a lower quartile of ≥4 were classified as having reached consensus. RESULTS: Forty-eight panel members were recruited, with a high participation level at Round 2 (90%, n=43). Consensus was achieved for 12 of the 19 statements at Round 1. The 7 remaining statements were revised, with 2 new statements, resulting in 9 statements at Round 2. Four statements reached consensus at Round 2. The final list includes 16 clinical guidance statements; 9 relating to assessment, 3 to OAT drug choice and dosing, 1 to take-away doses, 2 to overdose prevention and 1 to the continuation of e-prescriptions. CONCLUSIONS: A wide range of stakeholders involved in the delivery and receipt of OAT agreed on 16 clinical guidance statements for inclusion in OAT clinical guidelines as we move beyond the pandemic, rather than reverting to pre-pandemic guidelines. The agreed statements relate to facilitating safe access to OAT with minimal waiting time, supporting patient-centred care to promote health and well-being, and preventing drug overdose. Notably, consensus was not achieved for OAT drug dosage and frequency of urine testing during the stabilisation and maintenance phase of care.

Transmission of SARS-CoV-2 by children: a rapid review, 30 December 2019 to 10 August 2020.

BackgroundThe role of children in the transmission of SARS-CoV-2 during the early pandemic was unclear.AimWe aimed to review studies on the transmission of SARS-CoV-2 by children during the early pandemic.MethodsWe searched MEDLINE, Embase, the Cochrane Library, Europe PubMed Central and the preprint servers medRxiv and bioRxiv from 30 December 2019 to 10 August 2020. We assessed the quality of included studies using a series of questions adapted from related tools. We provide a narrative synthesis of the results.ResultsWe identified 28 studies from 17 countries. Ten of 19 studies on household and close contact transmission reported low rates of child-to-adult or child-to-child transmission. Six studies investigated transmission of SARS-CoV-2 in educational settings, with three studies reporting 183 cases from 14,003 close contacts who may have contracted COVID-19 from children index cases at their schools. Three mathematical modelling studies estimated that children were less likely to infect others than adults. All studies were of low to moderate quality.ConclusionsDuring the early pandemic, it appeared that children were not substantially contributing to household transmission of SARS-CoV-2. School-based studies indicated that transmission rates in this setting were low. Large-scale studies of transmission chains using data collected from contact tracing and serological studies detecting past evidence of infection would be needed to verify our findings.

Pharmacological interventions to prevent Covid-19 disease: A rapid review.

The aim of this rapid review was to determine the effectiveness of pharmacological interventions (excluding vaccines) to prevent coronavirus disease 2019 (Covid-19) or reduce the severity of disease. A systematic search of published peer-reviewed articles and non-peer-reviewed pre-prints was undertaken from 1 January 2020 to 17 August 2021. Four randomised controlled trials (RCTs) and one non-RCT were included; three trials (two RCTs and one non-RCT) tested ivermectin with or without carrageenan. While all reported some potential protective effect of ivermectin, these trials had a high risk of bias and the certainty of evidence was deemed to be 'very low'. One RCT tested bamlanivimab compared to placebo and reported a significantly reduced incidence of Covid-19 in the intervention group; this trial had a low risk of bias however the certainty of evidence was deemed 'very low'. The fifth RCT tested casirivimab plus imdevimab versus placebo and reported that the combination of monoclonal antibodies significantly reduced the incidence of symptomatic and asymptomatic SARS-CoV-2 infection, viral load, duration of symptomatic disease and the duration of a high viral load; this trial was deemed to have a low risk of bias, and the certainty of evidence was 'low'. The designations 'low' and 'very low' regarding the certainty of evidence indicate that the estimate of effect is uncertain and therefore is unsuitable for informing decision-making. At the time of writing, there is insufficient high quality evidence to support the use of pharmacological interventions to prevent Covid-19.

Quantifying the risk of SARS-CoV-2 reinfection over time.

Despite over 140 million SARS-CoV-2 infections worldwide since the beginning of the pandemic, relatively few confirmed cases of SARS-CoV-2 reinfection have been reported. While immunity from SARS-CoV-2 infection is probable, at least in the short term, few studies have quantified the reinfection risk. To our knowledge, this is the first systematic review to synthesise the evidence on the risk of SARS-CoV-2 reinfection over time. A standardised protocol was employed, based on Cochrane methodology. Electronic databases and preprint servers were searched from 1 January 2020 to 19 February 2021. Eleven large cohort studies were identified that estimated the risk of SARS-CoV-2 reinfection over time, including three that enrolled healthcare workers and two that enrolled residents and staff of elderly care homes. Across studies, the total number of PCR-positive or antibody-positive participants at baseline was 615,777, and the maximum duration of follow-up was more than 10 months in three studies. Reinfection was an uncommon event (absolute rate 0%-1.1%), with no study reporting an increase in the risk of reinfection over time. Only one study estimated the population-level risk of reinfection based on whole genome sequencing in a subset of patients; the estimated risk was low (0.1% [95% CI: 0.08-0.11%]) with no evidence of waning immunity for up to 7 months following primary infection. These data suggest that naturally acquired SARS-CoV-2 immunity does not wane for at least 10 months post-infection. However, the applicability of these studies to new variants or to vaccine-induced immunity remains uncertain.

Interventions in an Ambulatory Setting to Prevent Progression to Severe Disease in Patients With COVID-19: A Systematic Review.

OBJECTIVE: To conduct a systematic review on the effectiveness and safety of pharmacological and nonpharmacological interventions, in the ambulatory setting, aimed at preventing severe disease in patients with COVID-19. DATA SOURCES: Electronic databases (PubMed, EMBASE, and EuropePMC) were searched on January 6, 2021. STUDY SELECTION AND DATA EXTRACTION: A systematic review was conducted, adhering to PRISMA guidelines. The quality of individual trials was assessed using the Cochrane Risk-of-Bias Tool 2, and the certainty of evidence was assessed using GRADE. DATA SYNTHESIS: The collective search retrieved 3818 citations. Eight trials relating to 9 pharmacological interventions were identified. No evidence for nonpharmacological interventions was identified. Low certainty evidence of effectiveness in preventing severe disease was found for fluvoxamine (absolute difference: -8.7%; 95% CI: -1.8% to -16.4%) and bamlanivimab plus etesevimab (absolute difference: -4.9%; 95% CI: -0.8% to -8.9%). Both trials were limited by small sample sizes and short durations of follow-up. In addition, very low certainty evidence of effect was found for ivermectin plus doxycycline and sulodexide. Based on published data, insufficient evidence of effect was found for bamlanivimab (monotherapy), casirivimab plus imdevimab, ivermectin (monotherapy), nitazoxanide, and peginterferon lambda. RELEVANCE TO PATIENT CARE AND CLINICAL PRACTICE: This review assessed all ambulatory treatments for COVID-19 that may improve patient outcomes and reduce hospitalizations. CONCLUSION: Recent trials have shown promising results for a number of pharmacological agents to treat COVID-19 in the ambulatory setting. However, larger, more robust trials are needed to support the routine use of these agents outside of monitored clinical trials.

The effectiveness of non-contact thermal screening as a means of identifying cases of Covid-19: a rapid review of the evidence.

The aim of this rapid review is to summarise the evidence on non-contact thermal screening as a method through which to identify cases and reduce the spread of coronavirus disease (Covid-19). The rapid review was conducted in accordance with Cochrane guidelines, with a systematic search of published peer-reviewed articles and non-peer-reviewed pre-prints undertaken from 1 January 2000 up to 7 October 2020. Eleven studies were included. One observational study and two mathematical modelling studies were conducted in the context of the Covid-19 pandemic; the remaining studies were conducted during the influenza A pandemic (H1N1) 2009 (n = 7) or middle east respiratory syndrome (n = 1) pandemics. One systematic review and three rapid reviews were identified and screened for relevant studies. Evidence on the effectiveness of thermal screening contained within this review was limited to points of entry (i.e., airports); thus the applicability to other community settings is uncertain. Thermal screening, implemented as part of a composite of screening measures (self-report of relevant symptoms, contact/travel history), was ineffective in identifying infectious individuals and limiting the spread of disease. Based on limited, low certainty evidence, non-contact thermal screening is ineffective in limiting the spread of Covid-19.

Immune response following infection with SARS-CoV-2 and other coronaviruses: A rapid review.

In this review, we systematically searched and summarized the evidence on the immune response and reinfection rate following SARS-CoV-2 infection. We also retrieved studies on SARS-CoV and MERS-CoV to assess the long-term duration of antibody responses. A protocol based on Cochrane rapid review methodology was adhered to and databases were searched from 1/1/2000 until 26/5/2020. Of 4744 citations retrieved, 102 studies met our inclusion criteria. Seventy-four studies were retrieved on SARS-CoV-2. While the rate and timing of IgM and IgG seroconversion were inconsistent across studies, most seroconverted for IgG within 2 weeks and 100% (N = 62) within 4 weeks. IgG was still detected at the end of follow-up (49-65 days) in all patients (N = 24). Neutralizing antibodies were detected in 92%-100% of patients (up to 53 days). It is not clear if reinfection with SARS-CoV-2 is possible, with studies more suggestive of intermittent detection of residual RNA. Twenty-five studies were retrieved on SARS-CoV. In general, SARS-CoV-specific IgG was maintained for 1-2 years post-infection and declined thereafter, although one study detected IgG up to 12 years post-infection. Neutralizing antibodies were detected up to 17 years in another study. Three studies on MERS-CoV reported that IgG may be detected up to 2 years. In conclusion, limited early data suggest that most patients seroconvert for SARS-CoV-2-specific IgG within 2 weeks. While the long-term duration of antibody responses is unknown, evidence from SARS-CoV studies suggest SARS-CoV-specific IgG is sustained for 1-2 years and declines thereafter.

SARS-CoV-2 detection, viral load and infectivity over the course of an infection.

OBJECTIVES: To summarise the evidence on the detection pattern and viral load of SARS-CoV-2 over the course of an infection (including any asymptomatic or pre-symptomatic phase), and the duration of infectivity. METHODS: A systematic literature search was undertaken in PubMed, Europe PubMed Central and EMBASE from 30 December 2019 to 12 May 2020. RESULTS: We identified 113 studies conducted in 17 countries. The evidence from upper respiratory tract samples suggests that the viral load of SARS-CoV-2 peaks around symptom onset or a few days thereafter, and becomes undetectable about two weeks after symptom onset; however, viral loads from sputum samples may be higher, peak later and persist for longer. There is evidence of prolonged virus detection in stool samples, with unclear clinical significance. No study was found that definitively measured the duration of infectivity; however, patients may not be infectious for the entire duration of virus detection, as the presence of viral ribonucleic acid may not represent transmissible live virus. CONCLUSION: There is a relatively consistent trajectory of SARS-CoV-2 viral load over the course of COVID-19 from respiratory tract samples, however the duration of infectivity remains uncertain.